User: Rory Stark

gravatar for Rory Stark
Rory Stark1.7k
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Location:
CRUK, Cambridge, UK
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10 hours ago
Joined:
4 years, 2 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 299 results • page 1 of 30 • next >
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Answer: A: DiffBind R package issue
... Yes that is indeed a funny looking MA plot. It could be interesting to see the non-normalized version (bNormalized=FALSE in dba.plotMA) to make sure the normalisation process isn't doing something strange, but I doubt it. It is interesting that there are some clear outliers that are not identified ...
written 10 hours ago by Rory Stark1.7k
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Answer: A: Diffbind dba.report error
... Hi JB- What version of DiffBind are you using? This specific bug was addressed in the most recent release (2.4.0). There is a workaround. The problem is caused by the report for contrast 1 having only one element (R doesn't always deal well with single-row matrices/dataframes etc). The easiest way ...
written 10 hours ago by Rory Stark1.7k
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Answer: A: DiffBind R package issue
... When you run the analysis, it may be the case that no sites are identified as being differentially bound (DB) at a certain threshold. The warning message "No sites above threshold" is being generated by the call to dba.report(), indicating that there are no sites with FDR<- 0.01. So when you cal ...
written 1 day ago by Rory Stark1.7k
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Comment: C: Diffbind: getting the raw reads
... You can turn off the subtraction of control reads by setting bSubControl=FALSE in the call to dba.analyze(). -R ...
written 7 days ago by Rory Stark1.7k
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Answer: A: Low FDR for significant peaks in DiffBind output
... Hi Silvia- Sorry for the delay in responding -- I'm away on holiday and don't have access to a computer.  In he meantime one thing you can try is to set bCounts=TRUE in the call to dba.report() and check the read counts in the regions of interest. You may want to compare normalized and raw counts ...
written 7 days ago by Rory Stark1.7k
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Answer: A: DiffBind absence of reads
... The "official" set of sample data can be found at: http://DiffBind.starkhome.com This is also documented in the vignette.  Cheers- Rory ...
written 15 days ago by Rory Stark1.7k
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Answer: A: loading dba.plotVolcano in DiffBind
... The issue is the availability of a confidence statistic for the Y-axis. DiffBind only deals with contrasts comparing differential binding between two sample groups at a time. If you compare sample groups X and Y, you get confidence statistics (p-values,FDR) for each site, but you don't have them for ...
written 18 days ago by Rory Stark1.7k
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Comment: C: loading dba.plotVolcano in DiffBind
... Andrew, you are the first person besides me to use this feature. Thanks for noticing that I got the colors backwards! I won't be adding the hover option in this release, but it is a good idea. The function now silently returns the "red" sites as a GRanges object if you assign it to a variable. I've ...
written 23 days ago by Rory Stark1.7k
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Comment: C: loading dba.plotVolcano in DiffBind
... I've only tried installing from the source .tar.gz (it builds fine in R 3.3.0), so there may be an issue with mixing in a new binary on the old system. R can generally handle things if they are built in different versions, you just get a warning. One thing to try is to make sure not to load DiffBin ...
written 23 days ago by Rory Stark1.7k
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Answer: A: DiffBind: Plotting dba.Heatmap produces different clustering depending on whethe
... Hi Tim- It is difficult to say exactly what is going on without seeing the plots, but here are a few observations: As you are not specifying a contrast to dba.plotHeatmap(), you are getting a "global" clustering using all the sites, not just differentially bound ones. Is that what you intended? ...
written 23 days ago by Rory Stark1.7k

Latest awards to Rory Stark

Popular Question 7 days ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 11 weeks ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 11 weeks ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 12 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 12 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 14 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 16 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 17 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 18 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Scholar 18 months ago, created an answer that has been accepted. For A: Work with GRanges objects in DiffBind
Scholar 18 months ago, created an answer that has been accepted. For A: Clarification about the functionality of dba.count and dba.analyze
Scholar 18 months ago, created an answer that has been accepted. For A: subset of samples from dba object in DiffBind
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 21 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Scholar 23 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 24 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind dba.peakset() and consensus peaks
Scholar 24 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba

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